RetrogeneDB ID: retro_mmus_3427

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:21146842..21147334(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083892
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Atp1b3
• Ensembl ID: ENSMUSG00000032412
• Aliases: Atp1b3, AA409958, AI664000, AW212096
• Description: ATPase, Na+/K+ transporting, beta 3 polypeptide [Source:MGI Symbol;Acc:MGI:107788]

Sequence

>retro_mmus_3427
ATGACGAAGACTGAGAAGAAATCCTTCCACCAGAGCCTGGCCGAGTGGAAGCTGTTCATCTACAACCCGAGCAGCGGAGA
GTTTCTGGGGCGCACCTCCAAGAGCTGGGGTCTGATCTTGCTCTTCTACCTAGTTTTTTATGGGTTCTTGACTGCACTCT
TCACATTCACAATGTGGGCCATGCTCCAGACTCTGAATGATGAAGTTCTGAAATATCGAGACCAGATTCCTAGTCCAGGA
CTTACGGTTTTTCCCAAACCACAGACTGCCTTGGAATATACATTCAGCATGTCTGAGCCACAGACTTACGAAAAGTTGGT
TGAAGACCTGAAGAGTTTCCTAAAGCCATATTCTGTGGAAGAACAGAAGAACCTCACAAATTGTCCTGATGGAGCGCCTT
TTATTCAGCGTGGTCCTGACTATAGGGCATGTCAGTTTCCAGTCTCCTTGCTTGAAGAATGTAGTGGTGTGACTGATGCT
AATTTTGGCTAT

Alignment

ORF - retro_mmus_3427 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.73 %
• Parental protein coverage: 58.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTKTEKKSFHQSLAEWKLFIYNPSSGEFLGRTSKSWGLILLFYLVFYGFLAALFTFTMWAMLQTLNDEVP
          MTKTEKKSFHQSLAEWKLFIYNPSSGEFLGRTSKSWGLILLFYLVFYGFL.ALFTFTMWAMLQTLNDEV.
Retrocopy MTKTEKKSFHQSLAEWKLFIYNPSSGEFLGRTSKSWGLILLFYLVFYGFLTALFTFTMWAMLQTLNDEVL

Parental  KYRDQIPSPGLMVFPKPQTALEYTFSMSEPQTYKKLVEDLESFLKPYSVEEQKNLTSCPDGAPFIQHGPD
          KYRDQIPSPGL.VFPKPQTALEYTFSMSEPQTY.KLVEDL.SFLKPYSVEEQKNLT.CPDGAPFIQ.GPD
Retrocopy KYRDQIPSPGLTVFPKPQTALEYTFSMSEPQTYEKLVEDLKSFLKPYSVEEQKNLTNCPDGAPFIQRGPD

Parental  YRACQFPVSLLEECSGVTDANFGY
          YRACQFPVSLLEECSGVTDANFGY
Retrocopy YRACQFPVSLLEECSGVTDANFGY

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.05 RPM	86.02 RPM
SRP007412_cerebellum	0.00 RPM	116.46 RPM
SRP007412_heart	0.00 RPM	50.90 RPM
SRP007412_kidney	0.00 RPM	85.31 RPM
SRP007412_liver	0.08 RPM	45.28 RPM
SRP007412_testis	0.14 RPM	347.62 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3427 was not detected

EST

No EST(s) were mapped for retro_mmus_3427 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_156715	305 libraries	211 libraries	287 libraries	116 libraries	153 libraries

The graphical summary, for retro_mmus_3427 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_3427 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3427 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014140	5 retrocopies	retro_btau_1136, retro_btau_1322, retro_btau_1743, retro_btau_318, retro_btau_920,
Choloepus hoffmanni	ENSCHOG00000007515	4 retrocopies	retro_chof_1000, retro_chof_1421, retro_chof_2393, retro_chof_2445,
Callithrix jacchus	ENSCJAG00000001981	1 retrocopy	retro_cjac_309,
Cavia porcellus	ENSCPOG00000003739	4 retrocopies	retro_cpor_1181, retro_cpor_1468, retro_cpor_1506, retro_cpor_222,
Equus caballus	ENSECAG00000019885	2 retrocopies	retro_ecab_1084, retro_ecab_468,
Homo sapiens	ENSG00000069849	2 retrocopies	retro_hsap_1387, retro_hsap_2263,
Loxodonta africana	ENSLAFG00000010553	1 retrocopy	retro_lafr_815,
Mus musculus	ENSMUSG00000032412	2 retrocopies	retro_mmus_2174, retro_mmus_3427 ,
Nomascus leucogenys	ENSNLEG00000004663	1 retrocopy	retro_nleu_1286,
Otolemur garnettii	ENSOGAG00000008662	1 retrocopy	retro_ogar_2284,
Procavia capensis	ENSPCAG00000013927	1 retrocopy	retro_pcap_350,
Pongo abelii	ENSPPYG00000014169	1 retrocopy	retro_pabe_1953,
Pan troglodytes	ENSPTRG00000015476	2 retrocopies	retro_ptro_1603, retro_ptro_951,
Rattus norvegicus	ENSRNOG00000011501	2 retrocopies	retro_rnor_2571, retro_rnor_789,
Sus scrofa	ENSSSCG00000011676	3 retrocopies	retro_sscr_889, retro_sscr_945, retro_sscr_95,
Ictidomys tridecemlineatus	ENSSTOG00000013235	1 retrocopy	retro_itri_1663,
Tupaia belangeri	ENSTBEG00000001004	1 retrocopy	retro_tbel_3620,
Tarsius syrichta	ENSTSYG00000000222	1 retrocopy	retro_tsyr_330,
Tursiops truncatus	ENSTTRG00000012038	1 retrocopy	retro_ttru_333,